lib/CXGN/Page/Secretary.pm

   1 package CXGN::Page::Secretary;
   2 use strict;
   3
   4 use CXGN::Login;
   5 use CXGN::People;
   6 use CXGN::Contact;
   7 use CXGN::Cookie;
   8 use CXGN::UserPrefs;
   9 use CXGN::DB::Connection;
  10 use CXGN::Page::Widgets;
  11 use HTML::Entities;
  12
  13 use base('CXGN::Page');
  14
  15 sub new {
  16     my $class=shift;
  17         my $page_name = shift;
  18         my $author = shift;
  19
  20         ## I've decided to make the Secretary Page module create the default database handle for the Page-calling script
  21
  22         my $self = $class->SUPER::new($page_name, $author);
  23
  24         my $dbh = CXGN::DB::Connection->new();
  25         $dbh->do("SET SEARCH_PATH=tsearch2,public,sgn_people");
  26         $self->{dbh} = $dbh;
  27
  28         my %evidefs;
  29         my $evidef_q = $dbh->prepare("SELECT * FROM ara_evidef");
  30         $evidef_q->execute();
  31         while(my $row = $evidef_q->fetchrow_hashref) {
  32                 $evidefs{$row->{code}} = $row->{description};
  33         }
  34         $self->{evicode2definition} = \%evidefs;
  35         $self->{hotlist_button_ids} = {};
  36
  37         #The project name will still be SGN for cookie compatibility, but we use the Secretary Page/VHost file
  38         $self->{page_module}="CXGN::Page::VHost::Secretary";
  39         eval "require $self->{page_module}";
  40         if($@){
  41                 die("Secretary VHost Page module ($self->{page_module}) not found");
  42         }
  43         $self->{page_object}=$self->{page_module}->new($self->{dbh});
  44         $self->fetch_arguments();
  45
  46         return $self;
  47 }
  48
  49 sub fetch_arguments {
  50         my $self = shift;
  51         (               $self->{gene}, $self->{searchQuery}, $self->{noCheck}, $self->{leftBound}, $self->{querySize},
  52                         $self->{referenceGene}, $self->{prevQuery}, $self->{prevLB}, $self->{physicalMode}, $self->{username},
  53                         $self->{pass}, $self->{logout}, $self->{newUser}, $self->{passRep}, $self->{email},
  54                         $self->{fname}, $self->{lname}, $self->{org}, $self->{error404}
  55         )
  56                 = map { HTML::Entities::decode($_) }
  57                         $self->get_encoded_arguments
  58                         (
  59                         'g', 'query', 'nocheck', 'lb', 'qsize',
  60                         'referenceGene', 'prevQ', 'prevLB', 'physicalMode', 'username',
  61                         'password', 'logout', 'newuser', 'passwordrep', 'email',
  62                         'fname', 'lname', 'org', 'error404'
  63                         );
  64
  65         if(!($self->{leftBound} =~ /^\d+$/) || $self->{leftBound} <= 0) {
  66                 $self->{leftBound} = 1;
  67         }
  68
  69         $self->{gene} ||= "";
  70         $self->{searchQuery} ||= "";
  71         #$self->{searchQuery} =~ s/^\s*(.*?)\s*$/$1/;
  72
  73         my $querySize = $self->{querySize};
  74         if(defined $querySize && (!($querySize =~ /^\d+$/) || $querySize<=0)) { undef $querySize }
  75         $self->{querySize} = $querySize;
  76
  77         my $physicalMode = 0;
  78         if($self->{referenceGene}) { $physicalMode = 1}
  79         $self->{physicalMode} ||= $physicalMode;
  80 }
  81
  82 ### User account functions #########################################
  83
  84 sub login {
  85         my $self = shift;
  86         my ($username, $password) = ($self->{username}, $self->{pass});
  87         $username ||= '';
  88         $password ||= '';
  89         my $login_controller = CXGN::Login->new({NO_REDIRECT=>1});
  90         my $login_info=$login_controller->login_user($username,$password);
  91         $self->{login_info} = $login_info;
  92         return $login_info;
  93 }
  94
  95 sub logout {
  96         my $logout_controller = CXGN::Login->new({NO_REDIRECT=>1});
  97         $logout_controller->logout_user();
  98 }
  99
 100 sub new_user {
 101         my $self = shift;
 102
 103         my ($first_name, $last_name, $username, $password, $confirm_password, $email_address)
 104                 = ($self->{fname}, $self->{lname}, $self->{username}, $self->{pass}, $self->{passRep}, $self->{email});
 105
 106         if ($username) {
 107         #
 108         # check password properties...
 109         #
 110         my @fail = ();
 111         if (length($username) < 7) {
 112             push @fail, "Username is too short. Username must be 7 or more characters";
 113           } else {
 114             # does user already exist?
 115             #
 116               my $existing_login = CXGN::People::Login -> get_login($username);
 117
 118               if ($existing_login->get_username()) {
 119                   push @fail, "Username \"$username\" is already in use. Please pick a different username.";
 120               }
 121
 122           }
 123           if (length($password) < 7) {
 124             push @fail, "Password is too short. Password must be 7 or more characters";
 125           }
 126           if ("$password" ne "$confirm_password") {
 127             push @fail, "Password and confirm password do not match.";
 128           }
 129           if ($password eq $username) {
 130             push @fail, "Password must not be the same as your username.";
 131           }
 132           if ($email_address !~ m/[^\@]+\@[^\@]+/) {
 133             push @fail, "Email address is invalid.";
 134           }
 135
 136
 137           if (@fail) {
 138             return new_user_fail(\@fail);
 139           }
 140
 141           my $confirm_code = $self->tempname();
 142           my $new_user = CXGN::People::Login->new();
 143           $new_user -> set_username($username);
 144           $new_user -> set_password($password);
 145           $new_user -> set_pending_email($email_address);
 146           $new_user -> set_confirm_code($confirm_code);
 147 #         $new_user -> set_disabled('unconfirmed account');
 148           $new_user -> store();
 149
 150           #this is being added because the person object still uses two different objects, despite the fact that we've merged the tables
 151                 my $person_id=$new_user->get_sp_person_id();
 152                 my $new_person=CXGN::People::Person->new($person_id);
 153                 $new_person->set_first_name($first_name) if ($first_name);
 154                 $new_person->set_last_name($last_name) if ($last_name);
 155                 $new_person->store();
 156
 157                 $self->{person_id} = $person_id;
 158                 return "success";
 159         }
 160         else {
 161                 return "Username not provided";
 162         }
 163 }
 164
 165 sub new_user_fail {
 166         my ($fail_ref) = @_;
 167
 168         my $fail_str = "";
 169         foreach ( @{$fail_ref} ) {
 170                 $fail_str .= "<li>$_</li>\n"
 171         }
 172
 173         return <<END_HEREDOC;
 174
 175 <table summary="" width=80% align=center>
 176 <tr><td style='color:black'>
 177 <p style='color:#dd4444'>Your account could not be created for the following reasons</p>
 178
 179 <ul>
 180 $fail_str
 181 </ul>
 182 </td></tr>
 183 <tr><td><br /></td></tr>
 184 </table>
 185 END_HEREDOC
 186
 187 }
 188
 189 sub set_hotlist {
 190         my $self = shift;
 191         unless($self->{hotlist}){
 192                 $self->{hotlist} = $self->{page_object}->get_hotlist();
 193         }
 194
 195         if($self->{hotlist}){
 196                 $self->{hotlist_content} = $self->{hotlist}->get_item_contents();
 197         }
 198         return $self->{hotlist};
 199 }
 200
 201 sub get_login_info {
 202         my $self = shift;
 203
 204         my $just_logged_in = 0;  #we can't check a cookie that we just set, so use this to properly display page elements on first page-load of login
 205         my $login_warning = '';
 206         my $extra_notification = '';
 207         my $login_info_person_id = 0;
 208         my $login_info;
 209
 210
 211         if($self->{newUser}){
 212                 $login_warning = $self->new_user();
 213                 $login_info = $self->login();
 214                 $extra_notification = "New account with the username \"$self->{username}\" created!";
 215         }
 216         elsif($self->{username}){
 217                 $login_info = $self->login();
 218                 if($login_info->{incorrect_password}) { $login_warning = "You provided an incorrect password for this account." }
 219                 if($login_info->{account_disabled}) {
 220                         $login_warning =  "Your account has been disabled.  Please contact <a href='mailto:support\@sgn.cornell.edu'>support\@sgn.cornell.edu</a>";
 221                 }
 222                 if($login_info->{duplicate_cookie_string}) { $login_warning = "A duplicate cookie string has been issued (rare).  Please try again." }
 223                 if($login_info->{logins_disabled}) { $login_warning = "Sorry, logins have been temporarily disabled on this system" }
 224                 if(!$login_warning) {
 225                         $login_warning = "success";
 226                         $login_info_person_id = $login_info->{person_id};
 227                 }
 228         }
 229
 230         # overrides username login_info handler, which has to remain in place to make warnings (i should change this)
 231         my $loginh = CXGN::Login->new({NO_REDIRECT=>1});
 232         my $extra_warning;
 233         if(my $sp_person_id = $loginh->has_session()){
 234                 $login_info = $loginh->get_login_info();
 235                 $self->{validUser} = 1;
 236         }
 237         if($login_warning eq "success") {
 238                 $login_warning = '';
 239                 $just_logged_in = 1;
 240                 $self->{validUser} = 1;
 241         }
 242
 243         $self->{person_id} = $login_info->{person_id};
 244         $self->{cookie_string} = $login_info->{cookie_string};
 245         $self->{user_prefs} = $login_info->{user_prefs};
 246
 247         if($login_warning) { $login_warning .= "<br>" }
 248
 249         $self->{just_logged_in} = $just_logged_in;
 250         $self->{login_warning} = $login_warning;
 251         if($extra_notification) { $login_warning = $extra_notification }
 252
 253         if($self->{person_id}){
 254 #makes sure that cookie and database user_pref string are current and agreeable on initial login or when loading any page.  This is important when the user changes a preference, then jumps to a page in which UserPrefs ISN'T used, so the database will stil be updated with the new client cookie string.
 255                 my $prefh = CXGN::UserPrefs->new( $self->{dbh}, $self->{person_id} );
 256                 $self->{user_prefs} = $prefh->get_user_pref_string();
 257         }
 258
 259         #logout is done last since we want to sync up the userprefs that were set before the logout button was clicked
 260         if($self->{logout}){
 261                 $self->logout();
 262         }
 263
 264
 265
 266         return $login_warning;
 267
 268 }
 269
 270 ### CXGN::Page over-riding functions  #############
 271 sub get_system_message {
 272         my $self = shift;
 273         my $system_message='';
 274         if(my $message_file=$self->{vhost_object}->get_conf('system_message_file'))
 275     {
 276         my $message_text=CXGN::Tools::File::file_contents($message_file);
 277         $system_message.="<span class=\"developererrorbox\">$message_text</span><br />";
 278     }
 279     unless($self->{vhost_object}->get_conf('production_server'))
 280     {
 281         my $connection_test=CXGN::DB::Connection->new_no_connect();
 282         $system_message.="<span class=\"developererrorbox\">Viewing the ".$connection_test->dbname." database on ".$connection_test->dbhost.", ".$connection_test->dbbranch." branch</span>\n";
 283     }
 284         else { die("This site is not ready to go live yet!");}
 285
 286         return $system_message;
 287 }
 288
 289 sub get_header {
 290         my $self = shift;
 291 #       $self->{request}->send_http_header("text/html");
 292         if($self->{content_title}){ $self->{page_title} .= ": " . $self->{content_title} }
 293
 294         my $system_message = $self->get_system_message();
 295         my $login_warning = $self->get_login_info();
 296
 297         my $login_panel = $self->{page_object}->login_panel($self->{gene}, $self->{searchQuery});
 298
 299         my $html_head = $self->html_head();
 300
 301         my $user_bar = $self->{page_object}->user_bar
 302                                                                         (
 303                                                                                 $self->{gene}, $self->{searchQuery}, $self->{just_logged_in}, $self->{person_id}, $self->{error404}
 304                                                                         );
 305         my $body_tag = "<body>";
 306
 307         my $notifier = CXGN::Page::Widgets::notifier();
 308
 309         if($self->{content_title} =~ /Home/i) { $body_tag = "<body onload='document.getElementById(\"query_focus\").focus()'>" }
 310 return<<HTML;
 311 <html>
 312 $html_head
 313 $body_tag
 314 <center>
 315 <div id='userbar_container' style='width:100%'>
 316 <table style='width:100%; margin-bottom:5px;'>
 317 <tr>
 318         <td style='text-align:left'>
 319         $system_message
 320         </td>
 321         <td style='text-align:right'>
 322         $user_bar
 323         </td>
 324 </tr>
 325 </table>
 326 </div>
 327 <span id='login_warning' style='color:#dd4444; font-size:1.05em'>$login_warning</span>
 328 $login_panel
 329 </center>
 330 <noscript>
 331 <center>
 332 <span style='font-size:0.9em; color:#990000'>
 333 <a href='/documents/howtojs.html' style='color:#993355'><b>Javascript</b></a> (and cookies) must be enabled for logging in, hotlists, and dynamic effects
 334 </span>
 335 </center>
 336 </noscript>
 337 <center>
 338 $notifier
 339 </center>
 340
 341 <!--/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/| BEGIN PAGE CONTENT |/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/-->
 342
 343 HTML
 344 }
 345
 346 sub header {
 347         my $self = shift;
 348         ($self->{page_title}, $self->{content_title}, $self->{extra_head_stuff}) = @_;
 349         unless($self->{page_title})
 350     {
 351         $self->{page_title}=$self->{name};
 352     }
 353         print $self->get_header();
 354 }
 355
 356 sub footer {
 357         my $self = shift;
 358         my $extra_footer_stuff = shift;
 359         print $self->get_footer($extra_footer_stuff);
 360 }
 361
 362 sub get_footer {
 363         my $self = shift;
 364         my $extra_footer_stuff = shift;
 365         $extra_footer_stuff||='';
 366 return <<HTML;
 367 </body>
 368 <head>
 369 <META HTTP-EQUIV="cache-control" CONTENT="no-store">
 370 <META HTTP-EQUIV="cache-control" CONTENT="no-cache">
 371 $extra_footer_stuff
 372 </head>
 373 </html>
 374 HTML
 375 }
 376
 377 sub jsan_render_includes {
 378         my ($self) = @_;
 379         return join("\n",map { qq|<script language="JavaScript" src="$_" type="text/javascript"></script>| } $self->_jsan->uris);
 380 }
 381
 382 sub html_head
 383 {
 384     my $self=shift;
 385         $self->jsan_use(qw|CXGN.Base CXGN.UserPrefs CXGN.Effects CXGN.Hotlist CXGN.secretary|);
 386         my $jsanh = $self->_jsan();
 387         my $script_src = $self->jsan_render_includes();
 388         my $pathex = $jsanh->_class_to_file("CXGN.Effects");
 389
 390         #my $script_src = $self->jsan_render_includes();
 391     return<<HTML;
 392
 393 <head><title>$self->{page_title}</title>
 394
 395 <link rel="stylesheet" href="/documents/inc/secretary.css" TITLE="Secretary Default" TYPE="text/css" />
 396 <link rel="icon" href="favicon.ico" type="image/x-icon" />
 397 <link rel="shortcut icon" href="favicon.ico" type="image/x-icon" />
 398
 399 <META HTTP-EQUIV="cache-control" CONTENT="no-store" />
 400 <META HTTP-EQUIV="cache-control" CONTENT="no-cache" />
 401
 402 <script language='javascript'>
 403         var JSAN = {};
 404         JSAN.use = function () {};
 405
 406         //Global page variables for all scripts
 407         var thispage = location.href;
 408         var agi = '$self->{gene}';
 409         var query = '$self->{searchQuery}';
 410         var user_id = '$self->{person_id}';
 411         var cookie_string = '$self->{cookie_string}';
 412         var user_pref_string = '$self->{user_prefs}';
 413         var just_logged_in = '$self->{just_logged_in}';
 414         if(just_logged_in == '1') location.href = thispage;
 415
 416 </script>
 417 $script_src
 418 <!--transitional script
 419 $pathex
 420 <script language='javascript' src='/documents/inc/secretary.js'></script>
 421 -->
 422 </head>
 423
 424 HTML
 425 }
 426
 427 ## Secretary page elements ##################
 428 sub hotlist_button {
 429         my $self = shift;
 430         my $agi = shift;
 431         my $buttonText = "";
 432         my $enum = 0;
 433         my $i = 0;
 434         while($self->{hotlist_button_ids}->{"$agi:$i"}){
 435                 $i++;
 436         }
 437         $enum = $i;
 438         $self->{hotlist_button_ids}->{"$agi:$enum"} = 1;
 439
 440         if(!$self->{hotlist_content}) { $self->set_hotlist() }
 441         if($self->{validUser}){
 442                 my $in_hotlist = 0;
 443                 foreach(@{$self->{hotlist_content}}){
 444                         if ($_ eq $agi) { $in_hotlist = 1 }
 445                 }
 446                 if($in_hotlist) {
 447                         $buttonText .= <<HTML;
 448                         <img id='hotlistButton:$agi:$enum:imgAdd' src='/documents/img/secretary/hotlist_add.png' style='display:none' border=0 \>
 449                         <img id='hotlistButton:$agi:$enum:imgRemove' src='/documents/img/secretary/hotlist_remove.png' style='display:inline' border=0 \>
 450                         <a href='#' id='hotlistButton:$agi:$enum'
 451                                 onclick='Hotlist.remove(this.id, \"$agi\"); return false;'
 452                                 style='text-decoration:none'>Remove from Hotlist</a>
 453 HTML
 454                 }
 455                 else {
 456                         $buttonText .=  <<HTML;
 457                         <img id='hotlistButton:$agi:$enum:imgAdd' src='/documents/img/secretary/hotlist_add.gif' style='display:inline' border=0 \>
 458                         <img id='hotlistButton:$agi:$enum:imgRemove' src='/documents/img/secretary/hotlist_remove.gif' style='display:none'  border=0 \>
 459                         <a href='#' id='hotlistButton:$agi:$enum'
 460                                 onclick='Hotlist.add(this.id, \"$agi\");return false;'
 461                                 style='text-decoration:none'>Add to Hotlist</a>
 462 HTML
 463                 }
 464                 $buttonText .=  "&nbsp;<span id='hotlistWait:$agi:$enum' style='display:none'>...</span>";
 465         }
 466         else {
 467                 $buttonText .= <<HTML
 468                 <img src='/documents/img/secretary/hotlist_add.gif' border=0 \>
 469                 <a href='#' style='text-decoration:none'
 470                         onMouseOver='document.getElementById("hotlistGuest:$agi:$enum").style.display = "inline";'
 471                         onMouseOut='document.getElementById("hotlistGuest:$agi:$enum").style.display = "none";'
 472                         onclick='show_login();'>Add to Hotlist</a>&nbsp;
 473
 474         <span id='hotlistGuest:$agi:$enum' style='display:none;color:#aa3333' > Login to use hotlists</span>
 475 HTML
 476         }
 477         return $buttonText;
 478 }
 479
 480 sub navigation_info {
 481         my $self = shift;
 482         my $extraHREF = shift;
 483         my $querysize = $self->{querySize};
 484         my $lb = $self->{leftBound};
 485         my $searchquery = $self->{searchQuery};
 486         my $referenceGene = $self->{referenceGene};
 487         my $physicalMode = $self->{physicalMode};
 488         my $prevQuery = $self->{prevQuery};
 489         my $prevLB = $self->{prevLB};
 490
 491         if(!$physicalMode){
 492                 my $rb = $lb + 19;
 493                 if((defined $querysize) && ($querysize < 20 || ($lb + 19) > $querysize)){
 494                         $rb = $querysize;
 495                 }
 496                 my $navinfo = "<span style='font-size:1em'>Results <b>$lb</b> - <b>$rb</b> of ";
 497                 if(defined $querysize) {$navinfo .= "<b>$querysize</b><br>"}
 498                 else {$navinfo .= "<b>200+</b><br>"}
 499                 return $navinfo;
 500         }
 501         else {
 502
 503                 my %lowerbounds = ( 1=>10, 2=>10, 3=>10,4=>0,5=>10,M=>0,C=>0);
 504                 my %upperbounds = (1=>809, 2=>481, 3=>666, 4=>401, 5=>676, M=>14, C=>13);
 505                 my ($currentpos) = $searchquery =~ /AT[1-5MC]G(\d{1,3})/;
 506                 my ($refpos) = $referenceGene =~ /AT[1-5MC]G(\d{1,3})/;
 507                 my ($chromchar) = $searchquery =~ /AT([1-5MC])G/;
 508                 my $lower = $lowerbounds{$chromchar};
 509                 my $upper = $upperbounds{$chromchar};
 510                 $lower = int($lower / 5) * 5;
 511                 $currentpos = zeropadleft(int(zeropadright($currentpos)));
 512                 $refpos = zeropadleft(int($refpos));
 513                 my $navinfo = "<span style='font-size:1em'><b>$querysize</b> genes at the prefix <b>AT$chromchar" . "G$currentpos</b>";
 514                 $navinfo .= "&nbsp; &nbsp;<b style='letter-spacing:0px'>(";
 515                 my $i = $lower;
 516                 while ($i <= $upper){
 517                         my $pos = $i;
 518                         if(abs($pos-$currentpos)<3 || (abs($upper-$currentpos)<3 && abs($upper-$pos)<5)) {
 519                                 $pos = $currentpos;
 520                                 $navinfo .= "<span style='color:white;background-color:#000088'>|</span>";
 521                         }
 522                         elsif(abs($pos-$refpos)<3){
 523                                 $navinfo .= "<a title='" . zeropadleft($refpos) . "' href='query.pl?query=AT$chromchar" . "G" . zeropadleft($refpos);
 524                                 $navinfo .= "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'";
 525                                 $navinfo .= " style='text-decoration:none; background-color:#00AA00;font-weight:bold;color:white'>|</a>";
 526                         }
 527                         elsif(abs($upper-$pos)<5){
 528                                 $navinfo .= "<a title='" . zeropadleft($upper) . "' href='query.pl?query=AT$chromchar" . "G" . zeropadleft($upper);
 529                                 $navinfo .= "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'";
 530                                 $navinfo .= " style='text-decoration:none;font-weight:bold;'>|</a>";
 531                         }
 532                         else{
 533                                 $navinfo .= "<a title='" . zeropadleft($pos) . "' href='query.pl?query=AT$chromchar" . "G" . zeropadleft($pos);
 534                                 $navinfo .= "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'";
 535                                 $navinfo .= " style='font-weight:bold;text-decoration:none'>|</a>";
 536                         }
 537                         $i += 5;
 538                 }
 539
 540                 $navinfo .= ")</b></span>";
 541                 return $navinfo;
 542         }
 543 }
 544
 545 sub navigation_control {
 546         my $self = shift;
 547         my $prevReplace = shift;
 548         my $nextReplace = shift;
 549         my $extraHREF = shift;
 550         $extraHREF ||= "";
 551         my $lb = $self->{leftBound};
 552         my $query = $self->{searchQuery};
 553         my $nocheck = $self->{noCheck};
 554         my $referenceGene = $self->{referenceGene};
 555         my $physicalMode = $self->{physicalMode};
 556         my $querysize = $self->{querySize};
 557         my $prevQuery = $self->{prevQuery};
 558         my $prevLB = $self->{prevLB};
 559         my $navbar = "<span class='navbar'>";
 560
 561         if(!$physicalMode){     #standard search-relevance navigation
 562                 my $nextbound = 0;
 563
 564                 if($lb>1) {
 565                         if(defined $querysize){
 566                                 $nextbound = $lb - 20;
 567                                 if($nextbound != 1 || 1) {
 568                                         $navbar .=  "<a href='query.pl?query=$query&lb=1&qsize=$querysize&nocheck=$nocheck&prevQ=$prevQuery&prevLB=${prevLB}${extraHREF}'>&laquo; First</a> &nbsp;";
 569                                 }
 570                                 else {
 571                                         $navbar .= "<span style='color:grey'><u>&laquo; First</u> &nbsp;</span>";
 572                                 }
 573                                 $navbar .=  "<a href='query.pl?query=$query&lb=$nextbound&qsize=$querysize&nocheck=${nocheck}${extraHREF}'>&#8249; Prev</a> &nbsp;";
 574                         }
 575                         else{
 576                                 $nextbound = $lb - 20;
 577                                 if($nextbound != 1 || 1) { ##still deciding whether to grey-out if unnecessary
 578                                         $navbar .= "<a href='query.pl?query=$query&lb=1&nocheck=${nocheck}${extraHREF}'>&laquo; First</a> &nbsp;";
 579                                 }
 580                                 else {
 581                                         $navbar .= "<span style='color:grey'><u>&laquo; First</u> &nbsp;</span>";
 582                                 }
 583                                 $navbar .= "<a href='query.pl?query=$query&lb=$nextbound&nocheck=${nocheck}${extraHREF}'>&#8249; Prev</a> &nbsp;";
 584                         }
 585
 586                 }
 587                 else {
 588                         $navbar .= "<span style='color:grey'><u>&laquo; First</u> &nbsp;<u>&#8249; Prev</u> &nbsp;</span>";
 589                 }
 590
 591                 if((!defined $querysize) || (($querysize - $lb) >= 20)){
 592                         $nextbound = $lb + 20;
 593                         my $lastbound;
 594                         if(defined $querysize) {
 595                                 $navbar .= "<a href='query.pl?query=$query&lb=$nextbound&qsize=$querysize&nocheck=${nocheck}${extraHREF}'>Next &#8250;</a> &nbsp;";
 596                         }
 597                         else {
 598                                 $navbar .= "<a href='query.pl?query=$query&lb=$nextbound&nocheck=${nocheck}${extraHREF}'>Next &#8250;</a> &nbsp;"
 599                         }
 600                         if(!defined $querysize) {$lastbound = $lb + 200 }
 601                         elsif($querysize%20) {$lastbound = $querysize - $querysize%20 + 1 }
 602                         else {$lastbound = $querysize - 19 }
 603
 604                         if(defined $querysize)  {
 605                                 if($lastbound != $nextbound || 1){
 606                                         $navbar .= "<a href='query.pl?query=$query&lb=$lastbound&qsize=$querysize&nocheck=${nocheck}${extraHREF}'>Last &raquo;</a>";
 607                                 }
 608                                 else {
 609                                         $navbar .= "<span style='color:grey'><u>Last &raquo;</u></span>";
 610                                 }
 611                         }
 612                         else {
 613                                 $navbar .= "<a href='query.pl?query=$query&lb=$lastbound&nocheck=${nocheck}${extraHREF}'>Jump &raquo;</a>";
 614                         }
 615                 }
 616                 else {
 617                         $navbar .= "<span style='color:grey'><u>Next &#8250;</u> &nbsp;<u>Last &raquo;</u></span>";
 618                 }
 619         }
 620
 621         #gene pseudo-physical navigation
 622         else {
 623
 624                 ###Locus Boundaries####found by ordering locii in database#################
 625                 #               Lower Bounds:
 626                 #               1:01010
 627                 #               2:01031
 628                 #               3:01010
 629                 #               4:00010
 630                 #               5:01010
 631                 #               M:00010
 632                 #               C:00020
 633                 #
 634                 #               Upper Bounds
 635                 #               1:80990
 636                 #               2:48160
 637                 #               3:66658
 638                 #               4:40100
 639                 #               5:67640
 640                 #               M:01410
 641                 #               C:01310
 642                 my %lowerbounds = (1=>10, 2=>10, 3=>10,4=>0,5=>10,M=>0,C=>0);
 643                 my %upperbounds = (1=>809, 2=>481, 3=>666, 4=>401, 5=>676, M=>14, C=>13);
 644
 645                 my ($chrom) = $query =~ /(AT[1-5MC]G)/;
 646                 my ($chromchar) = $query =~ /AT([1-5MC])G/;
 647                 my ($location) = $query =~ /AT[1-5MC]G(\d{1,3})/;
 648
 649                 if(length($location)<1) { $location .= "000" }
 650                 elsif(length($location) == 1) { $location .= "00" }
 651                 elsif(length($location) ==2) { $location .= "0" }
 652                 $location = int($location);
 653                 my $jumpleft = $location - 10;
 654                 my $jumpright = $location + 10;
 655                 my $next = $location + 1;
 656                 my $prev = $location - 1;
 657
 658                 if($location > ($lowerbounds{$chromchar}+10)) {
 659                         $navbar .= "<a href='query.pl?query=$chrom" . zeropadleft($jumpleft) . "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'>&laquo; (x10)</a>&nbsp;&nbsp;";
 660                 }
 661                 else {
 662                         $navbar .= "<span style='color:grey'><u>&laquo; (x10)</u></span>&nbsp;&nbsp;";
 663                 }
 664                 if($location > $lowerbounds{$chromchar}) {
 665                         $navbar .= "<a href='query.pl?query=";
 666                         if($prevReplace){
 667                                 $navbar .= $prevReplace;
 668                         }
 669                         else {
 670                                 $navbar .= $chrom . zeropadleft($prev);
 671                         }
 672                         $navbar .= "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'>&#8249; Left</a>&nbsp;&nbsp;";
 673                 }
 674                 else {
 675                         $navbar .= "<span style='color:grey'><u>&#8249; Left</u></span>&nbsp;&nbsp;";
 676                 }
 677                 if($location < $upperbounds{$chromchar}) {
 678                         $navbar .= "<a href='query.pl?query=";
 679                         if($nextReplace){
 680                                 $navbar .= $nextReplace;
 681                         }
 682                         else {
 683                                 $navbar .= $chrom . zeropadleft($next);
 684                         }
 685                         $navbar .= "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'>Right &#8250;</a>&nbsp;&nbsp;";
 686                 }
 687                 else {
 688                         $navbar .= "<span style='color:grey'><u>Right &#8250;</u></span>&nbsp;&nbsp;";
 689                 }
 690                 if($location < ($upperbounds{$chromchar}-10)) {
 691                         $navbar .= "<a href='query.pl?query=$chrom" . zeropadleft($jumpright) . "&referenceGene=$referenceGene&prevQ=$prevQuery&prevLB=${prevLB}$extraHREF'>(x10) &raquo;</a>   ";
 692                 }
 693                 else {
 694                         $navbar .= "<span style='color:grey'><u>(x10) &raquo;</u></span>";
 695                 }
 696         }
 697         $navbar .= "</span>";
 698         return $navbar;
 699 }
 700
 701 ## Helper routines ##########################
 702 sub zeropadleft {
 703         my ($location) = @_;
 704
 705         if(length($location)==1) {
 706                 return "00" . $location;
 707         }
 708         elsif(length($location)==2) {
 709                 return "0" . $location;
 710         }
 711         else {
 712                 return "" . $location;
 713         }
 714 }
 715
 716 sub zeropadright {
 717         my ($location) = @_;
 718
 719         if(length($location)==1) {
 720                 return $location . "00";
 721         }
 722         elsif(length($location)==2) {
 723                 return $location . "0";
 724         }
 725         else {
 726                 return $location . "";
 727         }
 728 }
 729
 730
 731 ###
 732 1;#do not remove
 733 ###
 734